[med-svn] [gmap] 02/10: Updated version 2017-08-15 from 'upstream/2017-08-15'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Mon Sep 4 12:22:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 29b33b91e3f584c4d8413ce8c4947da25402851b
Merge: dab2e2b 67575fa
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Wed Aug 30 21:21:50 2017 +0200
Updated version 2017-08-15 from 'upstream/2017-08-15'
with Debian dir e8372eafa1e45acb137cc612311f036daac9aaa1
.gitignore | 1 -
ChangeLog | 674 +
Makefile.in | 5 +-
VERSION | 2 +-
config/ax_cpuid_intel.m4 | 11 +-
config/ax_cpuid_non_intel.m4 | 37 +-
config/ax_ext.m4 | 70 +-
configure | 957 +-
configure.ac | 222 +-
src/Makefile.am | 109 +-
src/Makefile.in | 7740 +++++-
src/block.c | 10 +-
src/chimera.c | 45 +-
src/chimera.h | 5 +-
src/chrom.c | 89 +-
src/cigar.c | 1647 ++
src/cigar.h | 33 +
src/config.h.in | 3 -
src/cpuid.c | 46 +-
src/datadir.c | 9 +-
src/diag.c | 96 +-
src/dynprog.c | 13 +-
src/dynprog.h | 3 +-
src/dynprog_cdna.c | 4 +-
src/dynprog_end.c | 53 +-
src/dynprog_end.h | 8 +-
src/dynprog_genome.c | 161 +-
src/dynprog_simd.c | 50 +-
src/dynprog_simd.h | 4 +
src/dynprog_single.c | 7 +-
src/genome.c | 12 +-
src/genome128_hr.c | 11583 +++++---
src/genome128_hr.h | 7 +-
src/get-genome.c | 328 +-
src/gmap.c | 1069 +-
src/gmap_select.c | 24 +
src/gmapl_select.c | 24 +
src/gsnap.c | 287 +-
src/gsnap_select.c | 24 +
src/gsnapl_select.c | 24 +
src/iit-read.c | 818 +-
src/iit-read.h | 19 +-
src/iit-write.c | 41 +-
src/iit-write.h | 5 +-
src/iit_get.c | 4 +-
src/indel.c | 125 +-
src/indel.h | 7 +-
src/indexdb.c | 21 +-
src/indexdb_hr.c | 2988 +-
src/interval.c | 66 +-
src/interval.h | 8 +-
src/intlist.c | 23 +-
src/intlist.h | 4 +-
src/intron.c | 43 +-
src/intron.h | 10 +-
src/junction.c | 7 +-
src/list.c | 32 +-
src/list.h | 3 +-
src/littleendian.h | 5 +-
src/maxent_hr.c | 10 +-
src/mem.h | 26 +-
src/merge-heap.c | 400 +
src/merge-heap.h | 19 +
src/merge.c | 1110 +
src/merge.h | 45 +
src/oligoindex_hr.c | 45074 ++++++++++---------------------
src/oligoindex_hr.h | 54 +-
src/outbuffer.c | 121 +-
src/outbuffer.h | 6 +-
src/output.c | 190 +-
src/output.h | 5 +-
src/pair.c | 2804 +-
src/pair.h | 55 +-
src/pairpool.c | 10 +-
src/parserange.c | 9 +-
src/popcount.c | 8 +-
src/popcount.h | 8 +-
src/samflags.h | 3 +-
src/samheader.c | 4 +-
src/samprint.c | 3330 +--
src/samprint.h | 43 +-
src/sarray-read.c | 7486 +----
src/sarray-read.h | 35 +-
src/{sarray-read.c => sarray-search.c} | 2145 +-
src/sarray-search.h | 32 +
src/sequence.c | 36 +-
src/sequence.h | 4 +-
src/shortread.c | 83 +-
src/smooth.c | 35 +-
src/spanningelt.c | 36 +-
src/spanningelt.h | 6 +-
src/stage1hr.c | 3513 ++-
src/stage1hr.h | 10 +-
src/stage2.c | 1863 +-
src/stage3.c | 1572 +-
src/stage3.h | 30 +-
src/stage3hr.c | 2378 +-
src/stage3hr.h | 31 +-
src/substring.c | 459 +-
src/substring.h | 55 +-
src/table.c | 28 +-
src/table.h | 4 +-
src/uniqscan.c | 14 +-
tests/Makefile.in | 5 +-
util/Makefile.am | 12 +-
util/Makefile.in | 27 +-
util/gmap_build.pl.in | 66 +-
util/gtf_transcript_splicesites.pl.in | 490 +
108 files changed, 50304 insertions(+), 53210 deletions(-)
--
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